On 12/1/13 8:04 AM, shahab shariati wrote:
Dear Justin

Very thanks for your reply

I will slow pulling by changing pull_rate1 from 0.01 to 0.001
and pull_k1 from 1000 to 100.

I have a basic question. Before minimization, where should I put drug
molecule? into water molecules or into lipid bilayer? Should I put drug
molecule in the specific position?


If you're trying to pull it into/across the bilayer, the most intuitive thing to do is place it within the water and pull it across to set up your configurations. You can do it however you like.

-Justin

--
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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